To facilitate storage and download all databases are
GNU
Zip (gzip, *.gz) compressed.

About the data

The following types of data dumps are available on the FTP site.

FASTA

FASTA sequence databases of Ensembl gene, transcript and protein
model predictions. Since the
FASTA format does not permit sequence annotation,
these database files are mainly intended for use with local sequence
similarity search algorithms. Each directory has a README file with a
detailed description of the header line format and the file naming
conventions.

The header line in an FASTA dump files containing DNA sequence
consists of the following attributes :
coord_system:version:name:start:end:strand
This coordinate-system string is used in the Ensembl API to retrieve
slices with the SliceAdaptor.

Flat files allow more extensive sequence annotation by means of
feature tables and contain thus the genome sequence as annotated by
the automated Ensembl
genome
annotation pipeline. Each nucleotide sequence record in a flat
file represents a 1Mb slice of the genome sequence. Flat files are
broken into chunks of 1000 sequence records for easier downloading.

All Ensembl MySQL databases are available in text format as are
the SQL table definition files. These can be imported into to any SQL
database for a local
installation of a mirror
site. Generally, the FTP directory tree contains one one directory per
database. For more information about these databases and their
Application Programming Interfaces (or APIs) see the
API section.

GTF

Gene sets for each species. These files include annotations of
both coding and non-coding genes. This file format is
described here.

EMF flatfile dumps (variation and comparative data)

Alignments of resequencing data are available for several species as
Ensembl Multi Format (EMF) flatfile dumps. The accompanying README
file describes the file format.

Also, the same format is used to dump whole-genome multiple alignments
as well as gene-based multiple alignments and phylogentic trees used
to infer Ensembl orthologues and paralogues. These files are available
in the ensembl_compara database which will be found in
the mysql
directory.

GVF (variation data)

GVF (Genome Variation Format) is a simple tab-delimited format derived
from GFF3 for variation positions across the genome.
There are GVF files for different types of variation data (e.g.
somatic variants, structural variants etc). For more information see
the "README" files in the GVF directory.

BED format files (comparative data)

Constrained elements calculated using GERP are available in BED
format. For more information see the accompanying README file.

BED format is a simple line-based format. The first 3 mandatory columns
are: